2016
Yuen, Douglas; Cartwright, Stephen; Jacob, Christian
Eukaryo: Virtual Reality Simulation of a Cell Proceedings Article
In: Proceedings of the 2016 Virtual Reality International Conference, pp. 3:1–3:4, ACM, Laval, France, 2016, ISBN: 978-1-4503-4180-6.
Abstract | Links | BibTeX | Tags: biological simulation, cell metabolism, eukaryotic cell, game engine, machinery of life, virtual reality
@inproceedings{Yuen:2016:EVR:2927929.2927931,
title = {Eukaryo: Virtual Reality Simulation of a Cell},
author = {Douglas Yuen and Stephen Cartwright and Christian Jacob},
doi = {10.1145/2927929.2927931},
isbn = {978-1-4503-4180-6},
year = {2016},
date = {2016-01-01},
urldate = {2016-01-01},
booktitle = {Proceedings of the 2016 Virtual Reality International Conference},
pages = {3:1--3:4},
publisher = {ACM},
address = {Laval, France},
series = {VRIC '16},
abstract = {Eukaryo is an interactive, 3-dimensional, simulated bio-molecular world that allows users to explore the complex environment within a biological cell. Eukaryo was developed using Unity, leveraging the capabilities and high performance of a commercial game engine. Through the use of MiddleVR, our tool can support a wide variety of interaction platforms including 3D virtual reality (VR) environments, such as head-mounted displays and large scale immersive visualization facilities.
Our model demonstrates key structures of a generic eukaryotic cell. Users are able to use multiple modes to explore the cell, its structural elements, its organelles, and some key metabolic processes. In contrast to textbook diagrams and even videos, Eukaryo immerses users directly in the biological environment giving a more effective demonstration of how cellular processes work, how compartmentalization affects cellular functions, and how the machineries of life operate.},
keywords = {biological simulation, cell metabolism, eukaryotic cell, game engine, machinery of life, virtual reality},
pubstate = {published},
tppubtype = {inproceedings}
}
Eukaryo is an interactive, 3-dimensional, simulated bio-molecular world that allows users to explore the complex environment within a biological cell. Eukaryo was developed using Unity, leveraging the capabilities and high performance of a commercial game engine. Through the use of MiddleVR, our tool can support a wide variety of interaction platforms including 3D virtual reality (VR) environments, such as head-mounted displays and large scale immersive visualization facilities.
Our model demonstrates key structures of a generic eukaryotic cell. Users are able to use multiple modes to explore the cell, its structural elements, its organelles, and some key metabolic processes. In contrast to textbook diagrams and even videos, Eukaryo immerses users directly in the biological environment giving a more effective demonstration of how cellular processes work, how compartmentalization affects cellular functions, and how the machineries of life operate.
Our model demonstrates key structures of a generic eukaryotic cell. Users are able to use multiple modes to explore the cell, its structural elements, its organelles, and some key metabolic processes. In contrast to textbook diagrams and even videos, Eukaryo immerses users directly in the biological environment giving a more effective demonstration of how cellular processes work, how compartmentalization affects cellular functions, and how the machineries of life operate.
2006
Jacob, Christian; Steil, Scott; Bergmann, Karel P
The Swarming Body: Simulating the Decentralized Defenses of Immunity Conference
ICARIS, 2006.
Abstract | Links | BibTeX | Tags: biological simulation, immune system, LINDSAY
@conference{DBLP:conf/icaris/JacobSB06,
title = {The Swarming Body: Simulating the Decentralized Defenses of Immunity},
author = {Christian Jacob and Scott Steil and Karel P Bergmann},
url = {https://www.researchgate.net/profile/Christian_Jacob4/publication/221506532_The_Swarming_Body_Simulating_the_Decentralized_Defenses_of_Immunity/links/00463527b18e1c164f000000/The-Swarming-Body-Simulating-the-Decentralized-Defenses-of-Immunity.pdf},
doi = {10.1007/11823940_5},
year = {2006},
date = {2006-01-01},
urldate = {2006-01-01},
booktitle = {ICARIS},
pages = {52-65},
abstract = {We consider the human body as a well-orchestrated system of interacting swarms. Utilizing swarm intelligence techniques, we present our latest virtual simulation and experimentation environment, IMMS:VIGO::3D, to explore key aspects of the human immune system. Immune system cells and related entities (viruses, bacteria, cytokines) are represented as virtual agents inside 3-dimensional, decentralized and compartmentalized environments that represent primary and secondary lymphoid organs as well as vascular and lymphatic vessels. Specific immune system responses emerge as by-products from collective interac- tions among the involved simulated textquoteleftagentstextquoteright and their environment. We demonstrate simulation results for clonal selection and primary and secondary collective responses after viral infection, as well as the key response patterns encountered during bacterial infection. We see this simulation environment as an essential step towards a hierarchical whole-body simulation of the immune system, both for educational and research purposes.},
keywords = {biological simulation, immune system, LINDSAY},
pubstate = {published},
tppubtype = {conference}
}
We consider the human body as a well-orchestrated system of interacting swarms. Utilizing swarm intelligence techniques, we present our latest virtual simulation and experimentation environment, IMMS:VIGO::3D, to explore key aspects of the human immune system. Immune system cells and related entities (viruses, bacteria, cytokines) are represented as virtual agents inside 3-dimensional, decentralized and compartmentalized environments that represent primary and secondary lymphoid organs as well as vascular and lymphatic vessels. Specific immune system responses emerge as by-products from collective interac- tions among the involved simulated textquoteleftagentstextquoteright and their environment. We demonstrate simulation results for clonal selection and primary and secondary collective responses after viral infection, as well as the key response patterns encountered during bacterial infection. We see this simulation environment as an essential step towards a hierarchical whole-body simulation of the immune system, both for educational and research purposes.